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claude/update-taxonomy

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python-wrapper

sir-s3-update

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#221

#226

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v3.0.1

3d3f06be24 Fix candidates_formatted not found in print.mo_uncertainties() claude/update-taxonomy Claude 2026-05-06 18:43:00 +00:00
d23004641f Revert mo_matching_score.R; fix #288 in mo.R pre-filter instead Claude 2026-05-06 18:07:37 +00:00
b3b8d301ff Fix #287 (complex fallback) and #288 (species epithet scoring bias) Claude 2026-05-06 15:11:31 +00:00
155c2707ce add fn dr. M.S. (Matthijs) Berends 2026-05-05 12:41:45 +02:00
cead31bed0 prepare for morphology dr. M.S. (Matthijs) Berends 2026-05-04 22:57:42 +02:00
a5e8beff69 prepare for documentation dr. M.S. (Matthijs) Berends 2026-05-03 11:50:05 +02:00
9707450b89 Fix emend. author bug in get_author_year() and update ref documentation Claude 2026-05-02 14:34:45 +00:00
9447e0f2c2 Built site for AMR@3.0.1.9057: 0af3f84 gh-pages github-actions 2026-05-02 13:06:13 +00:00
284878ccca Python wrapper update python-wrapper github-actions[bot] 2026-05-02 12:59:12 +00:00
0af3f84655 (v3.0.1.9057) website fix main dr. M.S. (Matthijs) Berends 2026-05-02 14:56:26 +02:00
64753e9a16 Revamp beta NEWS.md section: concise, user-focused, telegram style (#284) Matthijs Berends 2026-05-02 10:31:33 +01:00
24f24ecaf8 Generalise interpretive rules for multi-guideline support (#268) (#283) Matthijs Berends 2026-05-01 18:38:51 +01:00
6fbd9e4b9f Built site for AMR@3.0.1.9055: f7e9294 github-actions 2026-04-30 17:52:11 +00:00
f7e9294bea Add parallel computing support to antibiogram() and wisca() (#281) (#282) Matthijs Berends 2026-04-30 18:41:56 +01:00
3a3027f171 Built site for AMR@3.0.1.9053: 23beebc github-actions 2026-04-30 08:07:42 +00:00
23beebc6c3 Migrate parallel computing in as.sir() from parallel:: to future/future.apply (#280) Matthijs Berends 2026-04-30 08:57:19 +01:00
425f4ad827 Built site for AMR@3.0.1.9052: 3f1b20c github-actions 2026-04-25 14:29:32 +00:00
3f1b20c304 (v3.0.1.9052) fix NEWS dr. M.S. (Matthijs) Berends 2026-04-25 16:21:31 +02:00
905dea2cf1 (v3.0.1.9051) fix NEWS dr. M.S. (Matthijs) Berends 2026-04-25 16:20:34 +02:00
e12355b4a8 Built site for AMR@3.0.1.9050: 8261b91 github-actions 2026-04-25 12:49:42 +00:00
8261b91b24 Fix custom reference_data support in as.sir() (#239) (PR #279) Matthijs Berends 2026-04-25 14:38:01 +02:00
cc4e9bab4b Built site for AMR@3.0.1.9050: 19157ce github-actions 2026-04-24 22:45:21 +00:00
19157ce718 Fix parallel computing in as.sir.data.frame (#276) Matthijs Berends 2026-04-25 00:34:38 +02:00
fdef91486c Built site for AMR@3.0.1.9048: e7780b6 github-actions 2026-04-22 06:33:22 +00:00
e7780b6d5f (v3.0.1.9048) fix #275 dr. M.S. (Matthijs) Berends 2026-04-22 08:16:44 +02:00
5dec3cfd25 Built site for AMR@3.0.1.9047: e0f8cf0 github-actions 2026-04-21 20:32:21 +00:00
e0f8cf0882 (v3.0.1.9047) fix #272 dr. M.S. (Matthijs) Berends 2026-04-21 22:11:40 +02:00
86b5ebf61f Built site for AMR@3.0.1.9045: 8ff5d44 github-actions 2026-04-21 20:03:58 +00:00
8ff5d4472a Add add_if_missing parameter to control NA handling in interpretive rules (#264) Matthijs Berends 2026-04-21 21:53:43 +02:00
f2e56dbc61 Built site for AMR@3.0.1.9044: fb8758f github-actions 2026-04-05 15:36:36 +00:00
fb8758f36b fix: convert Python lists to R vectors in wrapper generator (#270) Matthijs Berends 2026-04-05 17:26:21 +02:00
6d9934ac04 Built site for AMR@3.0.1.9044: 6c24718 github-actions 2026-04-04 10:03:48 +00:00
6c24718893 (v3.0.1.9044) fix old R version dr. M.S. (Matthijs) Berends 2026-04-04 11:51:50 +02:00
59b2ce5621 Built site for AMR@3.0.1.9043: 2254931 github-actions 2026-04-02 10:32:06 +00:00
225493192c (v3.0.1.9043) fix unit test dr. M.S. (Matthijs) Berends 2026-04-02 12:24:12 +02:00
d0fd6aa2cc Built site for AMR@3.0.1.9042: 26613d7 github-actions 2026-04-02 09:54:05 +00:00
26613d774b (v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules() dr. M.S. (Matthijs) Berends 2026-04-02 11:42:19 +02:00
d6c59896e9 Built site for AMR@3.0.1.9041: 3a736bc github-actions 2026-03-30 08:18:09 +00:00
3a736bc484 (v3.0.1.9041) add breakpoints 2026 dr. M.S. (Matthijs) Berends 2026-03-30 10:01:49 +02:00
d55d073ae9 Built site for AMR@3.0.1.9040: 9c95aa4 github-actions 2026-03-24 12:34:17 +00:00
9c95aa455c (v3.0.1.9040) fix MIC plotting dr. M.S. (Matthijs) Berends 2026-03-24 12:44:47 +01:00
2a8a1eda97 (v3.0.1.9039) cli fixes dr. M.S. (Matthijs) Berends 2026-03-23 10:38:28 +01:00
330f1a9dfe Built site for AMR@3.0.1.9038: 975a690 github-actions 2026-03-22 21:31:11 +00:00
975a690c10 (v3.0.1.9038) fix format inline dr. M.S. (Matthijs) Berends 2026-03-22 22:16:59 +01:00
c95646d39c Built site for AMR@3.0.1.9037: 3d1412e github-actions 2026-03-22 19:55:49 +00:00
3d1412e8c9 (v3.0.1.9037) improve cli messages dr. M.S. (Matthijs) Berends 2026-03-22 20:44:37 +01:00
3560dfd611 Built site for AMR@3.0.1.9036: 4171d5b github-actions 2026-03-20 16:11:30 +00:00
4171d5b778 (v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265) Matthijs Berends 2026-03-20 17:01:34 +01:00
ba003f3e23 Built site for AMR@3.0.1.9035: 8439e9c github-actions 2026-03-18 09:45:05 +00:00
8439e9c1d2 (v3.0.1.9035) fix loading in Positron dr. M.S. (Matthijs) Berends 2026-03-18 10:32:11 +01:00
33e262ed9b Built site for AMR@3.0.1.9034: 4dc3ec0 github-actions 2026-03-11 15:20:20 +00:00
4dc3ec0008 (v3.0.1.9034) Add amr_course() dr. M.S. (Matthijs) Berends 2026-03-11 16:07:31 +01:00
86a53a0901 Built site for AMR@3.0.1.9033: 353eaa3 github-actions 2026-03-09 11:08:33 +00:00
353eaa3f38 (v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group dr. M.S. (Matthijs) Berends 2026-03-09 11:57:36 +01:00
e7e8aa636e Built site for AMR@3.0.1.9032: cba315c github-actions 2026-03-08 19:46:45 +00:00
cba315c2e7 (v3.0.1.9032) fix unit tests dr. M.S. (Matthijs) Berends 2026-03-08 20:36:15 +01:00
1e81c2a013 Built site for AMR@3.0.1.9031: b6f8584 github-actions 2026-03-08 10:40:48 +00:00
b6f8584994 (v3.0.1.9031) fix MDRO for non-RStudio terminal dr. M.S. (Matthijs) Berends 2026-03-08 11:30:18 +01:00
ab5ce59112 Built site for AMR@3.0.1.9030: e2102c0 github-actions 2026-03-07 17:15:05 +00:00
e2102c081a (v3.0.1.9030) fix R 3.6 dr. M.S. (Matthijs) Berends 2026-03-07 18:07:24 +01:00
9af726dcaa mdro(): infer base drug resistance from drug+inhibitor combination co… (#263) Matthijs Berends 2026-03-07 18:06:55 +01:00
daab605ca4 (v3.0.1.9028) fix unique CIDs dr. M.S. (Matthijs) Berends 2026-03-06 18:53:42 +01:00
c0a394008e (v3.0.1.9027) Fixes #252 and add documentation update regarding #253 dr. M.S. (Matthijs) Berends 2026-03-06 13:10:33 +01:00
599302f0bd Built site for AMR@3.0.1.9026: 60e8f2b github-actions 2026-03-06 11:55:19 +00:00
60e8f2bae6 (v3.0.1.9026) fix ab_group(NA) dr. M.S. (Matthijs) Berends 2026-03-06 12:41:27 +01:00
acc807a02c Built site for AMR@3.0.1.9023: 4e3ea95 github-actions 2026-03-04 08:11:02 +00:00
4e3ea95fbd Claude/fix issue 245 (#262) Matthijs Berends 2026-03-04 08:59:44 +01:00
3c74d99480 Built site for AMR@3.0.1.9022: 0311834 github-actions 2026-03-03 14:52:15 +00:00
0311834035 Merge branch 'main' of https://github.com/msberends/AMR dr. M.S. (Matthijs) Berends 2026-03-03 15:44:34 +01:00
b6211931f8 (v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR) dr. M.S. (Matthijs) Berends 2026-03-03 15:41:08 +01:00
6f0dc96d0d Built site for AMR@3.0.1.9021: 2c21eba github-actions 2026-02-27 16:25:41 +00:00
2c21eba04c add CLAUDE.md with project context for Claude Code (#261) Matthijs Berends 2026-02-27 17:13:11 +01:00
f0ec851466 Built site for AMR@3.0.1.9021: 12cf144 github-actions 2026-02-12 19:45:10 +00:00
12cf144b19 (v3.0.1.9021) add guideline to resistance() and susceptibility() dr. M.S. (Matthijs) Berends 2026-02-12 20:34:06 +01:00
c149bb1f65 Built site for AMR@3.0.1.9020: 499c830 github-actions 2026-02-09 12:53:52 +00:00
499c830ee7 (v3.0.1.9020) unit test fixes dr. M.S. (Matthijs) Berends 2026-02-09 13:16:36 +01:00
8b71d0eb99 Built site for AMR@3.0.1.9019: ba4c159 github-actions 2026-02-08 22:40:23 +00:00
ba4c159154 (v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules() dr. M.S. (Matthijs) Berends 2026-02-08 23:15:40 +01:00
0551ea51cb Built site for AMR@3.0.1.9018: 2df2911 github-actions 2026-01-16 10:08:12 +00:00
2df2911cf4 (v3.0.1.9018) fixes #249 updates AB groups dr. M.S. (Matthijs) Berends 2026-01-16 10:57:03 +01:00
86f19c7576 Built site for AMR@3.0.1.9017: fd50c51 github-actions 2026-01-08 13:12:14 +00:00
fd50c51543 (v3.0.1.9017) fix documentation dr. M.S. (Matthijs) Berends 2026-01-08 14:03:02 +01:00
39894d56c9 Built site for AMR@3.0.1.9016: cfd1922 github-actions 2026-01-08 11:36:31 +00:00
cfd1922dd9 (v3.0.1.9016) fix unit test dr. M.S. (Matthijs) Berends 2026-01-08 12:29:08 +01:00
a4edc69618 Built site for AMR@3.0.1.9015: 7df28bc github-actions 2026-01-08 09:35:29 +00:00
7df28bce28 (v3.0.1.9015) fix translations dr. M.S. (Matthijs) Berends 2026-01-08 10:21:48 +01:00
e2ba695c2c Built site for AMR@3.0.1.9014: 7b9c151 github-actions 2026-01-07 14:17:42 +00:00
7b9c151241 (v3.0.1.9014) try-again fix dr. M.S. (Matthijs) Berends 2026-01-07 15:10:21 +01:00
bb2e68890c Built site for AMR@3.0.1.9013: 85e8e81 github-actions 2026-01-07 12:40:00 +00:00
85e8e814e8 (v3.0.1.9013) fix translations dr. M.S. (Matthijs) Berends 2026-01-07 13:30:54 +01:00
70d4d19168 Built site for AMR@3.0.1.9012: fa827f2 github-actions 2026-01-07 10:08:49 +00:00
fa827f27f4 (v3.0.1.9012) fix translations dr. M.S. (Matthijs) Berends 2026-01-07 11:00:58 +01:00
46858ec0a2 Built site for AMR@3.0.1.9008: 9d1b456 github-actions 2026-01-06 22:21:25 +00:00
9d1b4565f6 (v3.0.1.9008) fix #246 dr. M.S. (Matthijs) Berends 2026-01-06 23:11:34 +01:00
cfbbfb4fa5 (v3.0.1.9007) fix #246 dr. M.S. (Matthijs) Berends 2026-01-06 23:08:50 +01:00
01880ee020 Built site for AMR@3.0.1.9009: 35debe2 github-actions 2025-12-23 10:12:20 +00:00
35debe25ee (v3.0.1.9009) tidymodels vignette dr. M.S. (Matthijs) Berends 2025-12-23 11:02:26 +01:00
e9cf3d5572 (v3.0.1.9008) tidymodels vignette github-actions[bot] 2025-12-22 19:04:39 +01:00
1227e2c60c Built site for AMR@3.0.1.9007: a5c6aa9 github-actions 2025-12-22 08:48:41 +00:00
a5c6aa9fa8 (v3.0.1.9007) fix vignette github-actions[bot] 2025-12-22 09:34:58 +01:00